6JV7 | pdb_00006jv7

Chimeric Rat C5a

• PDB DOI: https://doi.org/10.2210/pdb6JV7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 2019-04-16 Released: 2020-04-22 
• Deposition Author(s): Zuo, C.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Chimeric protein probes for C5a receptors through fusion of anaphylatoxin C5a core region with a small-molecule antagonist

Zuo, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.58 kDa 
• Atom Count: 1,387 
• Modeled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric-rC5a	A	77	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P08650 (Rattus norvegicus) Explore P08650  Go to UniProtKB:  P08650

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-anaphylatoxin C5a	B	77	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P08650 (Rattus norvegicus) Explore P08650  Go to UniProtKB:  P08650

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALN	A	L-PEPTIDE LINKING	C13 H13 N O2		ALA
ORN	A	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA
ZAL	A	D-PEPTIDE LINKING	C9 H17 N O2		--
DAL	B	D-PEPTIDE LINKING	C3 H7 N O2		--
DAR	B	D-PEPTIDE LINKING	C6 H15 N4 O2		--
DAS	B	D-PEPTIDE LINKING	C4 H7 N O4		--
DCY	B	D-PEPTIDE LINKING	C3 H7 N O2 S		--
DGL	B	D-PEPTIDE LINKING	C5 H9 N O4		--
DGN	B	D-PEPTIDE LINKING	C5 H10 N2 O3		--
DHI	B	D-PEPTIDE LINKING	C6 H10 N3 O2		--
DIL	B	D-PEPTIDE LINKING	C6 H13 N O2		--
DLE	B	D-PEPTIDE LINKING	C6 H13 N O2		--
DLY	B	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DPN	B	D-PEPTIDE LINKING	C9 H11 N O2		--
DPR	B	D-PEPTIDE LINKING	C5 H9 N O2		--
DSG	B	D-PEPTIDE LINKING	C4 H8 N2 O3		--
DSN	B	D-PEPTIDE LINKING	C3 H7 N O3		--
DTH	B	D-PEPTIDE LINKING	C4 H9 N O3		--
DTY	B	D-PEPTIDE LINKING	C9 H11 N O3		--
DVA	B	D-PEPTIDE LINKING	C5 H11 N O2		--
MED	B	D-PEPTIDE LINKING	C5 H11 N O2 S		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.709	α = 90
b = 57.609	β = 90
c = 81.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Zuo, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	21532004
National Natural Science Foundation of China	China	91753205
National Natural Science Foundation of China	China	81621002
National Natural Science Foundation of China	China	21621003

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations